Tuesday, July 22, 2014
7th Paper PRESENTERS: Singh, J.; Chuaqui, C.; Boriack-Sjodin, P.; Lee, W.; Pontz, T.; Corbley, M.; Cheung, H.; Arduini, R.; Mead, J.; Newman, M.; Papadatos, J.; Bowes, S.; Josiah, S.; Ling, L., Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). Bioorg Med Chem Lett 2003, 13 (24), 4355-9. SinghVirtualTGFbetaBioorgMedChemLett2003.pdf
Presentation Order:
1st Week: none
2nd Week: DHFR paper - Nikki
3rd Week: Hsp90 - Carolyn, Chris
4th Week: Bacterial FAS - Andrei + Technical Presentation on PCR by Zain
5th Week: HisG - Cidia
6th Week - July: Candida - Andee + Research Presentation:
7th Week - July: HIV - Luis + Research Presentation: Charina & Chris, Brianna
8th Week - July: TGFB1 - Charina, Hailey + Research Presentation: Nikki & Carolyn, Luis & Zain, Andee
9th Week - July: UBC-L3 Briana + Research Presentation: Cidia,Hailey
HSers: Sarah, Minsu, Braxton, Roshni, Caroline W
A few days before you present it, send a draft of your presentation to Dr. B & meet to discuss in person
Upload your presentation before class to the GroupMeetingSlides/GroupMeetingSlides/StudentPresentations folder on Google Docs
Guidelines:
prepare a 10 minute powerpoint slide show
Start out with a title slide that has the Journal Article name, Journal Name and Authors on it.
Put YOUR name on title slide also since you are presenting.
Put the date of the presentation on their as well - and something like 'VDS Summer Journal Club'
Create an introduction that provides a broad perspective for the specific [[#|work]] being presented. For example, if you are presenting a [[#|paper]] on a new protein, you should provide some background on the protein family and what it does. Don't assume that everyone in your audience knows the background. You can use your own content if you like - along with that given by the authors.
Include a picture or image that helps give a visual for the background.
Include any statistics about the disease and its prevalence (this is motivation)
Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any techniques that we are currently using in our lab?
Include graphs and figures from the paper.Use the SNIPPING tool in Windows to get pictures of the graphs, etc. from the paper. However, you will want a few 'original' images of your own. You can also make your own cartoons and schematic diagrams or show relevant pictures to get across the point.
Make an effort to explain what is going on in the figures (try to include all of them - but you can leave out some if they do not contribute to a 10 minute presentation)
Be sure to actually show the images and figures from the paper when talking about them (include some type of caption)
Do the results suggest any additional experiments that would be the next.?
Feel free to interject your own viewpoint of the research (is it valuable, did they do anything you liked or disliked?)
Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically.
What is the most significant contribution of the specific work to the field in general?
Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
Go through your talk at least once as a practice run
TIPS:
for best contrast and readability - use black text on white background.
Put date on the title slide
When you get to a figure, explain what is on the X axis and what is on the Y-axis. This helps them understand the graph and also gives a little time for them to view the graph and digest what is being shown.
For graphs and tables - be sure to explicitly state what the 'take home message' of that figure is. What does the graph tell the reader?
Week 9
Tuesday, July 29, 2014
8th Paper PRESENTERS: Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K., Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. Bioorg Med Chem 2007, 15 (21), 6810-8. VDS_UBL3_bioorgmedchem2007.pdf
Technical Presentation by: ??? on PCR
COMPLETED PAPERS 2013 Summer:
Week 1
5th - no paper
Week 2
1st Paper
Tuesday June 10th NAME: Nikki W.
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496. Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Week 3
Tuesday, June 17, 2014 PRESENTER NAMES: Carolyn T. & Chris T.
Park, H.; Kim, Y. J.; Hahn, J. S., A novel class of Hsp90 inhibitors isolated by structure-based virtual screening. Bioorganic & Medicinal Chemistry Letters2007,17 (22), 6345-6349. ParkHsp90drugVirtualScreenBioorgMedChemLett2007.pdf
Week 4
Tuesday, June 24, 2014
3rd Paper PRESENTER NAMES: Andrei Zhang, Y.; White, S.; Rock, C., Inhibiting bacterial fatty acid synthesis. J Biol Chem2006,281 (26), 17541-4. FASII_review_jbc2006.pdf
Week 6
Tuesday, July 8, 2014
5th Paper
PRESENTERS:
Prasannan, P.; Suliman, H. S.; Robertus, J. D., Kinetic analysis of site-directed mutants of methionine synthase from Candida albicans. Biochem Biophys Res Commun2009,382 (4), 730-4.
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis2011,5 (11), e1411. LiWolbachia_ftsz_PLOSNegTropDis2011.pdf
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem2007,282 (27), 19905-16. HenrikksonMtDXR_JBiolChem2007.pdf
Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83. MochalkinVirtualScreeningBiotinCarboxylaseFASII_ACSCHemBiol2009.pdf
Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys2009,483 (1), 23-8. BaiRicinVirtualScreenToxicon2010.pdf
Week 5
Tuesday, July 1, 2014
4th Paper PRESENTERS: Cidia
Cho, Y.; Ioerger, T.; Sacchettini, J., Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J Med Chem2008,51 (19), 5984-92. ChoSacchettiniVirtualScreening_TB_HisG_JMedChem2008.pdf
Week 8
Tuesday, July 22, 20147th Paper
PRESENTERS:
Singh, J.; Chuaqui, C.; Boriack-Sjodin, P.; Lee, W.; Pontz, T.; Corbley, M.; Cheung, H.; Arduini, R.; Mead, J.; Newman, M.; Papadatos, J.; Bowes, S.; Josiah, S.; Ling, L., Successful shape-based virtual screening: the discovery of a potent inhibitor of the type I TGFbeta receptor kinase (TbetaRI). Bioorg Med Chem Lett 2003, 13 (24), 4355-9.
SinghVirtualTGFbetaBioorgMedChemLett2003.pdf
Presentation Order:
1st Week: none
2nd Week: DHFR paper - Nikki
3rd Week: Hsp90 - Carolyn, Chris
4th Week: Bacterial FAS - Andrei + Technical Presentation on PCR by Zain
5th Week: HisG - Cidia
6th Week - July: Candida - Andee + Research Presentation:
7th Week - July: HIV - Luis + Research Presentation: Charina & Chris, Brianna
8th Week - July: TGFB1 - Charina, Hailey + Research Presentation: Nikki & Carolyn, Luis & Zain, Andee
9th Week - July: UBC-L3 Briana + Research Presentation: Cidia, Hailey
HSers: Sarah, Minsu, Braxton, Roshni, Caroline W
Guidelines:
Week 9
Tuesday, July 29, 20148th Paper
PRESENTERS:
Hirayama, K.; Aoki, S.; Nishikawa, K.; Matsumoto, T.; Wada, K., Identification of novel chemical inhibitors for ubiquitin C-terminal hydrolase-L3 by virtual screening. Bioorg Med Chem 2007, 15 (21),
6810-8.
VDS_UBL3_bioorgmedchem2007.pdf
Technical Presentation by: ??? on PCR
COMPLETED PAPERS 2013 Summer:
Week 1
5th - no paperWeek 2
1st PaperTuesday June 10th
NAME: Nikki W.
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496.
Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Week 3
Tuesday, June 17, 2014PRESENTER NAMES: Carolyn T. & Chris T.
Park, H.; Kim, Y. J.; Hahn, J. S., A novel class of Hsp90 inhibitors isolated by structure-based virtual screening. Bioorganic & Medicinal Chemistry Letters 2007, 17 (22), 6345-6349.
ParkHsp90drugVirtualScreenBioorgMedChemLett2007.pdf
Week 4
Tuesday, June 24, 20143rd Paper
PRESENTER NAMES: Andrei
Zhang, Y.; White, S.; Rock, C., Inhibiting bacterial fatty acid synthesis. J Biol Chem 2006, 281 (26), 17541-4.
FASII_review_jbc2006.pdf
Week 6
Tuesday, July 8, 2014
5th Paper
PRESENTERS:
Prasannan, P.; Suliman, H. S.; Robertus, J. D., Kinetic analysis of site-directed mutants of methionine synthase from Candida albicans. Biochem Biophys Res Commun 2009, 382 (4), 730-4.
PrasannanPriya_MetSynthaseKinetic_RobertusBiochemBiophysResComm2009.pdf
Week 7
Tuesday, July 15, 20146th Paper
PRESENTERS:
Herschhorn, A.; Hizi, A., Virtual screening, identification, and biochemical characterization of novel inhibitors of the reverse transcriptase of human immunodeficiency virus type-1. J Med Chem 2008, 51 (18), 5702-13.
HerschhornHIVreversetranscriptaseVirtualScreenJMedChem2008.pdf
JournalClubQuestions072312_HIV.doc
Potential Papers:
Li, Z.; Garner, A. L.; Gloeckner, C.; Janda, K. D.; Carlow, C. K., Targeting the Wolbachia cell division protein FtsZ as a new approach for antifilarial therapy. PLoS Negl Trop Dis 2011, 5 (11), e1411.
LiWolbachia_ftsz_PLOSNegTropDis2011.pdf
Henriksson, L. M.; Unge, T.; Carlsson, J.; Aqvist, J.; Mowbray, S. L.; Jones, T. A., Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 2007, 282 (27), 19905-16.
HenrikksonMtDXR_JBiolChem2007.pdf
Tomlinson, S.; Malmstrom, R.; Watowich, S., New approaches to structure-based discovery of dengue protease inhibitors. Infect Disord Drug Targets 2009, 9 (3), 327-43.
TomlinsonWatowichDengueVirusInfectiousDisordersDrugTargets2009.pdf
Sacchettini, J.; Rubin, E.; Freundlich, J., Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol 2008, 6 (1), 41-52.
SacchettiniTuberculosis_DrugsVsBugsNatRevMicrobiol2008.pdf
Mochalkin, I.; Miller, J.; Narasimhan, L.; Thanabal, V.; Erdman, P.; Cox, P.; Prasad, J.; Lightle, S.; Huband, M.; Stover, C., Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem Biol 2009, 4 (6), 473-83.
MochalkinVirtualScreeningBiotinCarboxylaseFASII_ACSCHemBiol2009.pdf
Bai, Y.; Monzingo, A.; Robertus, J., The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys 2009, 483 (1), 23-8.
BaiRicinVirtualScreenToxicon2010.pdf
Week 5
Tuesday, July 1, 20144th Paper
PRESENTERS: Cidia
Cho, Y.; Ioerger, T.; Sacchettini, J., Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J Med Chem 2008, 51 (19), 5984-92.
ChoSacchettiniVirtualScreening_TB_HisG_JMedChem2008.pdf